Additional file 2.

Phylogenetic trees reconstructed from sequences obtained from patient P03 samples. Maximum likelihood tree reconstructed from full length NS5A region sequences obtained from samples of P03 (ETR) plus reference sequence of genotype 1b HCV-J. The number of 1000 permuted trees supporting a clade indicated when that proportion was greater than 70%. The same quasispecies are colored in red. Sequence with nonsense mutation is colored in blue. The clade selected for selective pressure analysis is indicated by a gray line.

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Jardim et al. BMC Infectious Diseases 2013 13:61   doi:10.1186/1471-2334-13-61